The bioBakery help forum

Multiple comparisons in


I’m looking at the help menu for and I see that there is an option for multiple comparisons, but I’m not understanding the distinctions.

Here is the option copied and pasted:

-s {0,1,2} set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison

These are my questions:

  1. Could please explain how not performing multiple corrections is the most strict?

  2. What is the difference between 1 and 2; they look identical to me except 1 is plural (independent comparisons) while 2 is singular (independent comparison).

Thank you,

Hello Samantha,

Thank you for reaching out to bioBakery support forum.

  • In this case “correction” is a little misleading, since setting the -s flag to 1 or 2 will make the p-value more permissive allowing multiple tests. By default, LEfSe will conservatively treat them as a single bulk test, hence more strict.
  • Apologies for the confusion on the ‘-s’ options flag.
    • 0 means no correction
    • 1 means correction for multiple independent tests
    • 2 means correction for multiple dependent tests.

The github repository has been updated as well with the typo fixed in the help menu ( Many thanks for pointing this out.